[BioC] snapCGH: T instead of TRUE, etc

[Ramon Diaz-Uriarte]

On Friday 16 March 2007 17:41, ma3mls at bath.ac.uk wrote:
> Hi Ramon,
>
> I've made and uploaded the changes you suggested.  All instances of T
> have been changed to TRUE in the appropriate source files.
>
> It's not an issue I've ever seen before.
>
Thanks Mike!

Actually, I was quite surprised because it does not show up in interactive 
usage, only while doing an R CMD check of a package that uses the 
non-homogeneous HMM functions. 

Best,

R.

> Mike Smith
>
> Quoting Ramon Diaz-Uriarte <rdiaz at cnio.es>:
> > Sorry, I forgot to say I am seeing this with versions 1.2.0 (BioC 1.9)
> > and 1.3.2 (BioC 2.0) of snapCGH (R-2.4., under Debian GNU/Linux).
> >
> > R.
> >
> > On Friday 16 March 2007 14:29, Ramon Diaz-Uriarte wrote:
> >> Dear All,
> >>
> >> Somewhat similar to what I reported before, with snapCGH I am getting
> >> errors, when building a package, that can be traced to errors in
> >> snapCGH. Specifically:
> >>
> >> The functions "find.param.{two.three..}" lead to errors such as
> >>
> >> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) :
> >>          T used instead of TRUE
> >> Error in matrix(c(1 - p1, p1, p2, 1 - p2), ncol = 2, b = T) :
> >>          recursive default argument reference
> >>
> >>
> >>
> >>
> >> And the functions Viterbi.{two.three..} also show similar problems, as
> >> in
> >>
> >> Error in matrix(nrow = K, ncol = n, b = T) :
> >>          T used instead of TRUE
> >> Error in matrix(nrow = K, ncol = n, b = T) :
> >>          recursive default argument referenc
> >>
> >> max(-1e+05, log(BFGS.output$prior[i]), na.rm = T)
> >>          T used instead of TRUE
> >>
> >>
> >>
> >>
> >> Once all the appropriate T are replaced by TRUE things are OK again.
> >>
> >>
> >>
> >> Best,
> >>
> >>
> >> R.
> >
> > --
> > Ramón Díaz-Uriarte
> > Statistical Computing Team
> > Centro Nacional de Investigaciones Oncológicas (CNIO)
> > (Spanish National Cancer Center)
> > Melchor Fernández Almagro, 3
> > 28029 Madrid (Spain)
> > Fax: +-34-91-224-6972
> > Phone: +-34-91-224-6900
> >
> > http://ligarto.org/rdiaz
> > PGP KeyID: 0xE89B3462
> > (http://ligarto.org/rdiaz/0xE89B3462.asc)
> >
> >
> >
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> >
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-- 
Ramón Díaz-Uriarte
Statistical Computing Team
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
(http://ligarto.org/rdiaz/0xE89B3462.asc)



**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en s...{{dropped}}